Hi Arek and thanks for your fast answer. You were rigth, I think it's a bug of the new version rc7. Yesterday Isaac and me were testing with release rc6 (and exactly the same schema) and solved the problem. Now we can see all relations (using the schema Editor) and if we check all the attributes from the web we receive the correct result of the query.
I think the problem could be during the transformation algorithm because when I add my database Biomart does not detect well the dimesion and submain tables. Thanks again, Joan ________________________________ De: Arek Kasprzyk [mailto:[email protected]] Enviado el: miércoles, 25 de enero de 2012 15:57 Para: PROTASIO, JOAN (IDIBAPS) CC: [email protected]; Yong Liang Asunto: Re: [BioMart Users] Problems adding source with constraints HI Joan, could you send me your DDL for your InnoDB schema please? We'll try to run it here and see what's going on cheers, a On Mon, Jan 23, 2012 at 8:40 PM, Arek Kasprzyk <[email protected]> wrote: Hi Joan, hmm .... this looks like a bug. I am cc'ing Yong, the MConfigurator expert, in case he wants to chip in and confirm that this is the case a On Mon, Jan 23, 2012 at 3:04 PM, <[email protected]> wrote: No I don't see the relations between tables, that's the problem. I also have tried to introduce only the main tables and I see that if I clik into the schema editor the other tables ( related with the constraints with main one) are introduced automatically by Biomart. In this case I can add a tab with a new entry and I can select the attributes of the main table (by the web) but unfortunately I neither see the relations nor the attributes of the other tables. Thanks -----Mensaje original----- De: [email protected] en nombre de Arek Kasprzyk Enviado el: lun 23/01/2012 17:01 Para: PROTASIO, JOAN (IDIBAPS) CC: [email protected] Asunto: Re: [BioMart Users] Problems adding source with constraints Hi Joan, do you see the relations between tables as well? a On Mon, Jan 23, 2012 at 10:44 AM, <[email protected]> wrote: > Hi Arek,**** > > ** ** > > well I'm choosing exactly the params source schema-> MySQL and I uncheck > the MYlSAM option because the schema of my local db works with InnoDB. > Afterthat I can see the source with all the tables involved in the schema. > Then if I select all of them I see various sources in my MartConfigurator. > **** > > ** ** > > Salutacions, **** > > Joan **** > > **** > > > ------------------------------------------------------------------------------ > **** > > **** > > Joan Protasio**** > > *Bioinformatics Unit: *http://bioinformatics.fcrb.es/bioinformatics/**** > > August Pi i Sunyer Biomedical Research Institute (IDIBAPS)**** > > Phone: 93.227.54.00 (Ext. 4522)**** > > C/ Rosselló 153**** > > 08036 Barcelona**** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > ------------------------------ > > *De:* [email protected] [mailto:[email protected]] *En > nombre de *Arek Kasprzyk > *Enviado el:* lunes, 23 de enero de 2012 16:04 > *Para:* PROTASIO, JOAN (IDIBAPS) > *CC:* [email protected] > *Asunto:* Re: [BioMart Users] Problems adding source with constraints**** > > ** ** > > Hi Joan,**** > > first of all you need to be aware that rc7 has not been officially > released. I am not sure how much testing gone into that. The last official > release is rc6. InnoDB should definitely work and behave just like oracle > or postgres. Are you choosing the right DB platform option ei NOT MySQL > MyISM?**** > > ** ** > > a**** > > ** ** > > On Mon, Jan 23, 2012 at 7:35 AM, <[email protected]> wrote:**** > > Hi all,**** > > **** > > I have problems adding new source from a local database. I am working with > the new Biomart version r7 and the local database works with constraints in > InnoDB format. If I try to add the source using the MartConfigurator and > click into the Schema Editor I don't see the relations like the mysql > constraints. I have read the paper "Biomart: a data federation framework." > and if I understand it well it says the source must be a relational db as > we have but I am not sure if the InnoDB format is good for Biomart. Could > you help me?**** > > **** > > Thanks a lot,**** > > **** > > Salutacions, **** > > Joan **** > > **** > > > ------------------------------------------------------------------------------ > **** > > **** > > Joan Protasio**** > > *Bioinformatics Unit: *http://bioinformatics.fcrb.es/bioinformatics/**** > > August Pi i Sunyer Biomedical Research Institute (IDIBAPS)**** > > Phone: 93.227.54.00 (Ext. 4522)**** > > C/ Rosselló 153**** > > 08036 Barcelona**** > > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users**** > > > > **** > > ** ** > > -- **** > > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead**** > > ** ** > -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead -- Arek Kasprzyk, MD, MSc, PhD BioMart Project Lead
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